I am so very sorry for the loss of your little ones. The pain is no easier be that you share their lives for only minutes or years. My prayers go with you to give you strength to make it through your losses.
I've not been following as closely as I should, your threads on the little ones so I am not sure of the ages of the little ones.
Unfortuneately, I can't really give you an answer as to why the little ones didn't make it. It could be that they were born premature and as such their digestive systems and/or other internal organs were not fully developed. We have had that happen from time to time - just about the time they begin to eat solid food, we lose them.
It could also be that the mother is killing them. Sometimes it is because she knows that something is wrong. Sometimes it is because they are not hers and she won't accept them. Sometimes, the mother just canibalizes the kittens. We had a mother do that one time - we too thought the first two kits who were smaller did have something wrong with them, so we let the remaining kits stay with her. Everything was fine for a day or two, then she killed another two kittens - these two were fat, healthy and eating well. At that point, even though they were really too young to take from her we did and bottle fed them and did their potty. We didn't want to risk her cleaning them and deciding to end their lives.
I did some research and found while it is not common place, there are some cats, especially purebreds who do kill their young. In the breeder community, these cats are not bred again and immediately spayed as chances are the mother will do it again. Research doesn't even to really seem to have an answer as to why it happens.
If I were you, I would take the remaining kitten from her. I'd just not take any chances. I'd not even let her preform grooming as if she is killing them she will take the first opportunity the kitten is returned to her to end his life.
Again, I am so sorry for your losses. Run with the wind little ones...... /mari
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